Routine processing of samples in the clinical setting involves formalin fixation and paraffin embedding. FFPE is a highly efficient method that is currently the standard in pathology suites. Formalin-fixed, paraffin-embedded (FFPE) tissues may be stored indefinitely at room temperature, and nucleic acids (both DNA and RNA) may be recovered from them decades after fixation, making FFPE tissues an important resource for molecular assays. However, better methods for developing FFPE materials that mimic actual patient specimens are needed to monitor the performance of molecular assays from FFPE materials and to develop appropriate quality control materials for these assays.